RNA is in the center of a major paradigm shift in Molecular Biology. Our previous perspective of a gene and the general concept for how a cell codes for proteins from DNA is still generally true for Bacteria and Archaea. However, in Eukaryotes, this perspective is being replaced with the notion that the complexity of an organism scales with the amount of RNA, not Protein, that is coded for in its genome. The functional properties of these RNA molecules are directly associated with their higher-order structure. Thus the prediction and identification of this structure from sequence will provide the foundation to understand the details of their function. Since the structural and functional properties of some recently discovered RNAs, such as different micro RNAs, are involved in the regulation of normal and aberrant cellular processes, studies that focus on RNA are expected to help determine the molecular biology for different diseases, and provide the basis for new drug therapies. Comparative analysis of RNA sequences and structures have been very successful in the elucidation of the entire structure of an RNA molecule and in the identification and characterization of the basic building blocks of RNA - structural motifs and structural elements. One of the PIs of this proposal, has established the "Comparative RNA Web (CRW)" site that disseminates collections and analysis of different types of comparative information for a few select RNA molecules. However, based on the significant increase in the number of sequences for the initial set of RNAs studied in this project, and now the significant increase in the number of RNAs that are being identified, we are developing a novel computational foundation intended to establish repeatable protocols for the comparative analysis of RNA sequences and structures. The current CRW Site will become a fully dynamic web service for the general scientific community to perform comparative analysis on their own RNAs, benefiting from the collection of RNA sequence and structure information and the computational infrastructure at the CRW Site. PUBLIC HEALTH RELEVANDE: Based on the functional importance of RNA and its higher-order structure, we are developing a novel computational foundation for the comparative analysis of RNA. This resource will benefit experimental laboratories that are studying RNAs that are associated with many different normal and aberrant processes in the cell, and could directly influence the development of new drug therapies.